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Search Results: 1 - 10 of 92758 matches for " Alan W. Walker "
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Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota
Philip Cooper, Alan W. Walker, Jorge Reyes, Martha Chico, Susannah J. Salter, Maritza Vaca, Julian Parkhill
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0076573
Abstract: Background The soil-transmitted helminth (STH), Trichuris trichiura colonises the human large intestine where it may modify inflammatory responses, an effect possibly mediated through alterations in the intestinal microbiota. We hypothesised that patent T. trichiura infections would be associated with altered faecal microbiota and that anthelmintic treatment would induce a microbiota resembling more closely that observed in uninfected individuals. Materials and Methods School children in Ecuador were screened for STH infections and allocated to 3 groups: uninfected, T. trichiura only, and mixed infections with T. trichiura and Ascaris lumbricoides. A sample of uninfected children and those with T. trichiura infections only were given anthelmintic treatment. Bacterial community profiles in faecal samples were studied by 454 pyrosequencing of 16 S rRNA genes. Results Microbiota analyses of faeces were done for 97 children: 30 were uninfected, 17 were infected with T. trichiura, and 50 with T. trichiura and A. lumbricoides. Post-treatment samples were analyzed for 14 children initially infected with T. trichiura alone and for 21 uninfected children. Treatment resulted in 100% cure of STH infections. Comparisons of the microbiota at different taxonomic levels showed no statistically significant differences in composition between uninfected children and those with T. trichiura infections. We observed a decreased proportional abundance of a few bacterial genera from the Clostridia class of Firmicutes and a reduced bacterial diversity among children with mixed infections compared to the other two groups, indicating a possible specific effect of A. lumbricoides infection. Anthelmintic treatment of children with T. trichiura did not alter faecal microbiota composition. Discussion Our data indicate that patent human infections with T. trichiura may have no effect on faecal microbiota but that A. lumbricoides colonisation might be associated with a disturbed microbiota. Our results also catalogue the microbiota of rural Ecuadorians and indicate differences with individuals from more urban industrialised societies.
Single Ion Adsorption and Switching in Nano-Electronics
Adam W. Bushmaker,Vanessa Oklejas,Don Walker,Alan R. Hopkins,Jihan Chen,Stephen B. Cronin
Physics , 2015,
Abstract: Single ion detection has, for many years, been the domain of large devices such as the Geiger counter, and studies on interactions of ionized gasses with materials have been limited to large systems. To date, there have been no reports on single gaseous ion interaction with microelectronic devices, and single neutral atom detection techniques have shown only small, barely detectable responses. Here, we report the first observation of single ion adsorption onto individual carbon nanotubes (CNTs), which, due to the severely restricted one-dimensional current path, experience discrete, quantized resistance increases of over two orders of magnitude. Only positive ions cause changes, by the mechanism of ion potential induced carrier depletion, which is supported by density functional and Landauer transport theory. Our observations reveal a new single-ion/CNT heterostructure with novel electronic properties, and demonstrate that as electronics are ultimately scaled towards the one-dimensional limit, atomic scale effects become increasingly important.
The validity of self-rated health as a measure of health status among young military personnel: evidence from a cross-sectional survey
Christopher K Haddock, Walker SC Poston, Sara A Pyle, Robert C Klesges, Mark W Vander Weg, Alan Peterson, Margaret Debon
Health and Quality of Life Outcomes , 2006, DOI: 10.1186/1477-7525-4-57
Abstract: The current study uses the population of active duty United States Air Force recruits (N = 31,108). Participants completed surveys that asked about health behaviors and health states and were rated their health on a continuum from poor to excellent.Ratings of health were consistently lower for those who used tobacco (F = 241.7, p < .001), reported binge drinking (F = 69.0, p < .001), reported drinking and driving (F = 19.4, p < .001), reported taking health risks (F = 109.4, p < .001), were depressed (F = 256.1, p < .001) and were overweight (F = 39.5, p < .001).Given the consistent relationship between self-rated overall health and factors important to military health and fitness, self-rated health appears to be a valid measure of health status among young military troops.Single item self-assessments of health are the most widely used measures of health status [1]. These self-assessments are used in many national surveys in the US, such as the National Health Interview Survey [2], National Health and Nutrition Examination Survey [3], and the Behavioral Risk Factor Surveillance System [4]. Self-rated health has been shown to be related to a number of important medical endpoints, such as health risk behaviors, disease states, disability, and mortality [1,5,6]. Self-ratings of health independently predict health parameters when compared to clinical evaluations and are sensitive to changes in health status [5,7].The United States (US) Military and its healthcare plan, TRICARE, use a variety of health self-reporting surveys to assess the health status of military members and other beneficiaries. These questionnaires are used to provide data on the health and healthcare needs of all military healthcare beneficiaries and to target specific health issues. For instance, the Health Care Survey of DoD Beneficiaries [8] assesses a broad range of healthcare issues such as the use of preventive services while the Health Enrollment Assessment Review (HEAR) was developed to identi
Review of "Ticks: Biology, Disease and Control" by Alan Bowman & Patricia Nuttall (eds.)
Alan R Walker
Parasites & Vectors , 2009, DOI: 10.1186/1756-3305-2-1
Abstract: Why study ticks? The standard answer is because they are economically and socially important as agents of disease. The corollary being that studying them is important. But ask a farmer in Uganda what she does about ticks on her Friesian diary herd – once a week dip in organophosphate! Or try sitting on a public health advisory board writing pamphlets about Lyme disease – wear long trousers tucked into socks! And if that is not discord enough, consider the increasing ethical problem of studying ticks. Even understanding their ecology needs information derived from feeding ticks on experimental animals – a nasty business indeed. Resolutions to this dissonance can be found in this book. Improvements in avoiding, preventing and curing vector associated diseases are at least as likely to derive, very unpredictably, from a broad advance in deep understanding, as they are from any specific applied study.Ticks are not insects, and the great clarification of their population dynamics in relation to pathogen transmission is a major advance for vector biology in general. Tick salivary glands are wonderful subjects for anatomical, physiological and biochemical study and as a source of pharmacological agents they are a deep and rich mine. The ability of ticks to evade host immune resistance provides routes for advances in fundamental immunology as well as inspiration for pharmaceuticals for human and animal treatment. Similarly the extraordinary adaptations of tick transmitted pathogens to exploit these immune evasions, or the normally functioning dermal hypersensitivity reactions to ticks, has greatly increased our understanding of the biology of viruses, bacteria and protozoa. The natural nidality of vector associated pathogens is strongly exemplified by tick spatial distributions. So the advent of geographical information systems, coupled with studies on microclimatic factors on tick survival, has consolidated understanding of a field of such public concern that we now get ne
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease
Alan W Walker, Jeremy D Sanderson, Carol Churcher, Gareth C Parkes, Barry N Hudspith, Neil Rayment, Jonathan Brostoff, Julian Parkhill, Gordon Dougan, Liljana Petrovska
BMC Microbiology , 2011, DOI: 10.1186/1471-2180-11-7
Abstract: Paired mucosal biopsies of inflamed and non-inflamed intestinal tissue from 6 CD (n = 12) and 6 UC (n = 12) patients were compared to biopsies from 5 healthy controls (n = 5) by in-depth sequencing of over 10,000 near full-length bacterial 16S rRNA genes. The results indicate that mucosal microbial diversity is reduced in IBD, particularly in CD, and that the species composition is disturbed. Firmicutes were reduced in IBD samples and there were concurrent increases in Bacteroidetes, and in CD only, Enterobacteriaceae. There were also significant differences in microbial community structure between inflamed and non-inflamed mucosal sites. However, these differences varied greatly between individuals, meaning there was no obvious bacterial signature that was positively associated with the inflamed gut.These results may support the hypothesis that the overall dysbiosis observed in inflammatory bowel disease patients relative to non-IBD controls might to some extent be a result of the disturbed gut environment rather than the direct cause of disease. Nonetheless, the observed shifts in microbiota composition may be important factors in disease maintenance and severity.Inflammatory bowel disease (IBD) encompasses both Crohn's disease (CD) and ulcerative colitis (UC), chronic inflammatory disorders of the gastrointestinal tract with developed world predominance and an incidence that has risen dramatically in the post-war period [1]. IBD manifests with symptoms such as severe diarrhoea, weight loss and debilitating abdominal pain, resulting in substantial morbidity and impairment in quality of life [2]. In both diseases visibly inflamed and non-inflamed areas of intestine can be identified at assessment by colonoscopy.The cause of both conditions is still speculative. Host genetics play a key role, with genetic factors more important for development of CD than UC [3,4], but genetic defects cannot wholly explain the increasing prevalence of IBD in recent years, suggesting
The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water
Abhilasha Karkey?,Thibaut Jombart?,Alan W. Walker,Corinne N. Thompson?,Andres Torres?,Sabina Dongol?,Nga Tran Vu Thieu?,Duy Pham Thanh?,Dung Tran Thi Ngoc?,Phat Voong Vinh
PLOS Neglected Tropical Diseases , 2016, DOI: 10.1371/journal.pntd.0004346
Abstract: One of the UN sustainable development goals is to achieve universal access to safe and affordable drinking water by 2030. It is locations like Kathmandu, Nepal, a densely populated city in South Asia with endemic typhoid fever, where this goal is most pertinent. Aiming to understand the public health implications of water quality in Kathmandu we subjected weekly water samples from 10 sources for one year to a range of chemical and bacteriological analyses. We additionally aimed to detect the etiological agents of typhoid fever and longitudinally assess microbial diversity by 16S rRNA gene surveying. We found that the majority of water sources exhibited chemical and bacterial contamination exceeding WHO guidelines. Further analysis of the chemical and bacterial data indicated site-specific pollution, symptomatic of highly localized fecal contamination. Rainfall was found to be a key driver of this fecal contamination, correlating with nitrates and evidence of S. Typhi and S. Paratyphi A, for which DNA was detectable in 333 (77%) and 303 (70%) of 432 water samples, respectively. 16S rRNA gene surveying outlined a spectrum of fecal bacteria in the contaminated water, forming complex communities again displaying location-specific temporal signatures. Our data signify that the municipal water in Kathmandu is a predominant vehicle for the transmission of S. Typhi and S. Paratyphi A. This study represents the first extensive spatiotemporal investigation of water pollution in an endemic typhoid fever setting and implicates highly localized human waste as the major contributor to poor water quality in the Kathmandu Valley.
Evidence for a Long-period Planet Orbiting Epsilon Eridani
Artie P. Hatzes,William D. Cochran,Barbara McArthur,Sallie L. Baliunas,Gordon A. H. Walker,Bruce Campbell,Alan W. Irwin,Stephenson Yang,Martin Kürster,Michael Endl,Sebastian Els,R. Paul Butler,Geoffrey W. Marcy
Physics , 2000, DOI: 10.1086/317319
Abstract: High precision radial velocity (RV) measurements spanning the years 1980.8--2000.0 are presented for the nearby (3.22 pc) K2 V star $\epsilon$ Eri. These data, which represent a combination of six independent data sets taken with four different telescopes, show convincing variations with a period of $\approx$ 7 yrs. A least squares orbital solution using robust estimation yields orbital parameters of period, $P$ = 6.9 yrs, velocity $K$-amplitude $=$ 19 {\ms}, eccentricity $e$ $=$ 0.6, projected companion mass $M$ sin $i$ = 0.86 $M_{Jupiter}$, and semi-major axis $a_2$ $=$ 3.3 AU. Ca II H&K S-index measurements spanning the same time interval show significant variations with periods of 3 and 20 yrs, yet none at the RV period. If magnetic activity were responsible for the RV variations then it produces a significantly different period than is seen in the Ca II data. Given the lack of Ca II variation with the same period as that found in the RV measurements, the long-lived and coherent nature of these variations, and the high eccentricity of the implied orbit, Keplerian motion due to a planetary companion seems to be the most likely explanation for the observed RV variations. The wide angular separation of the planet from the star (approximately 1 arc-second) and the long orbital period make this planet a prime candidate for both direct imaging and space-based astrometric measurements.
CutLHCO: A Consumer-Level Tool for Implementing Generic Collider Data Selection Cuts in the Search for New Physics
Joel W. Walker
Physics , 2012,
Abstract: A new computer program named CutLHCO is introduced, whose function is the implementation of generic data selection cuts on collider event specification files in the standardized .lhco format. This software is intended to fill an open market niche for a lightweight yet flexible "consumer-level" alternative to the ROOT data analysis framework. The primary envisioned application is as a filter on output produced by the PGS4 and DELPHES detector simulations, which are themselves lightweight alternatives to the GEANT4 based solutions favored by the large LHC experiments. All process control instructions are provided via a compact and powerful card file input syntax that efficiently facilitates the reasonable approximation of most event selection strategies and specialized discovery statistics commonly employed by the CMS and ATLAS collaborations. The structure, function, invocation and usage of the most recent CutLHCO 2.0 program version are documented thoroughly, including a detailed deconstruction of several example card file specifications. The associated software is simultaneously being made available for free public download.
Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups
Alan O. Marron, Michael Akam, Giselle Walker
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032867
Abstract: Background Nitrile hydratases are enzymes involved in the conversion of nitrile-containing compounds into ammonia and organic acids. Although they are widespread in prokaryotes, nitrile hydratases have only been reported in two eukaryotes: the choanoflagellate Monosiga brevicollis and the stramenopile Aureococcus anophagefferens. The nitrile hydratase gene in M. brevicollis was believed to have arisen by lateral gene transfer from a prokaryote, and is a fusion of beta and alpha nitrile hydratase subunits. Only the alpha subunit has been reported in A. anophagefferens. Methodology/Principal Findings Here we report the detection of nitrile hydratase genes in five eukaryotic supergroups: opisthokonts, amoebozoa, archaeplastids, CCTH and SAR. Beta-alpha subunit fusion genes are found in the choanoflagellates, ichthyosporeans, apusozoans, haptophytes, rhizarians and stramenopiles, and potentially also in the amoebozoans. An individual alpha subunit is found in a dinoflagellate and an individual beta subunit is found in a haptophyte. Phylogenetic analyses recover a clade of eukaryotic-type nitrile hydratases in the Opisthokonta, Amoebozoa, SAR and CCTH; this is supported by analyses of introns and gene architecture. Two nitrile hydratase sequences from an animal and a plant resolve in the prokaryotic nitrile hydratase clade. Conclusions/Significance The evidence presented here demonstrates that nitrile hydratase genes are present in multiple eukaryotic supergroups, suggesting that a subunit fusion gene was present in the last common ancestor of all eukaryotes. The absence of nitrile hydratase from several sequenced species indicates that subunits were lost in multiple eukaryotic taxa. The presence of nitrile hydratases in many other eukaryotic groups is unresolved due to insufficient data and taxon sampling. The retention and expression of the gene in distantly related eukaryotic species suggests that it plays an important metabolic role. The novel family of eukaryotic nitrile hydratases presented in this paper represents a promising candidate for research into their molecular biology and possible biotechnological applications.
A Duplex PCR-Based Assay for Measuring the Amount of Bacterial Contamination in a Nucleic Acid Extract from a Culture of Free-Living Protists
Alan O. Marron, Michael Akam, Giselle Walker
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061732
Abstract: Background Cultures of heterotrophic protists often require co-culturing with bacteria to act as a source of nutrition. Such cultures will contain varying levels of intrinsic bacterial contamination that can interfere with molecular research and cause problems with the collection of sufficient material for sequencing. Measuring the levels of bacterial contamination for the purposes of molecular biology research is non-trivial, and can be complicated by the presence of a diverse bacterial flora, or by differences in the relative nucleic acid yield per bacterial or eukaryotic cell. Principal Findings Here we describe a duplex PCR-based assay that can be used to measure the levels of contamination from marine bacteria in a culture of loricate choanoflagellates. By comparison to a standard culture of known target sequence content, the assay can be used to quantify the relative proportions of bacterial and choanoflagellate material in DNA or RNA samples extracted from a culture. We apply the assay to compare methods of purifying choanoflagellate cultures prior to DNA extraction, to determine their effectiveness in reducing bacterial contamination. Together with measurements of the total nucleic acid concentration, the assay can then be used as the basis for determining the absolute amounts of choanoflagellate DNA or RNA present in a sample. Conclusions The assay protocol we describe here is a simple and relatively inexpensive method of measuring contamination levels in nucleic acid samples. This provides a new way to establish quantification and purification protocols for molecular biology and genomics in novel heterotrophic protist species. Guidelines are provided to develop a similar protocol for use with any protistan culture. This assay method is recommended where qPCR equipment is unavailable, where qPCR is not viable because of the nature of the bacterial contamination or starting material, or where prior sequence information is insufficient to develop qPCR protocols.
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